3BYK

Crystal structure of B. subtilis levansucrase mutant D247A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OYG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	6.3	291	diammonium phosphate, sodium acetate, pH 6.3, MICRODIALYSIS, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.158	α = 90
b = 67.351	β = 90
c = 123.792	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAC Science DIP-2030		2003-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.07	30	99.5	0.038	0.038	25	8.7	26627	26627

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.14	99		0.068	0.068	25.1	8.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1OYG	2.1	30	25579	25579	1290	99.56	0.171	0.171	0.169	0.215	RANDOM	12.073

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.43			0.04		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.813
r_scangle_it	1.745
r_angle_refined_deg	1.193
r_scbond_it	1.133
r_angle_other_deg	0.773
r_mcangle_it	0.621
r_mcbond_it	0.34
r_symmetry_hbond_refined	0.285
r_symmetry_vdw_other	0.28
r_nbd_other	0.238
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.141
r_xyhbond_nbd_refined	0.125
r_nbtor_other	0.08
r_chiral_restr	0.078
r_metal_ion_refined	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3439
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling